User: Vitis

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Vitis2.3k
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8 years, 5 months ago
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A plant geneticist from a taxonomist and naturalist background. Now trying to bridge classic genetics and evolutionary biology with ever-expanding genomic data and bioinformatic tools.

Posts by Vitis

<prev • 324 results • page 1 of 33 • next >
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Answer: A: BWA Mem -M flag (mark split hits) effect on structural variation calling
... I've never used -M option for structural variant calling. Based on this BWA thread, you may lose supplementary mapping information by using -M option, because -M may label split reads as duplicates and strip the secondary/supplementary mapping information. I believe at least some SV tools use split ...
written 4 weeks ago by Vitis2.3k
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Answer: A: Variant Annotation and prioritization
... The annotation tools snpEff would be a good start. You may also look at PyVCF to extract genotypes from VCF files. http://snpeff.sourceforge.net https://pyvcf.readthedocs.io/en/latest/ ...
written 5 weeks ago by Vitis2.3k
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Comment: C: Mutant Transcript is higher than the WT. What may be the reason?
... One simple way to try this is: for each sample, count total number of reads mapped within the gene boundaries, divide by the number of total reads, then multiply 1 million. This gives you the reads/million for this gene in this sample, so you can compare this value across samples. Basically, for eac ...
written 5 weeks ago by Vitis2.3k
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Comment: C: snpEff build not working with gff3
... For GFF3 annotations downloaded from Ensembl (which should meet all GFF3 standard and pass GFF3 validations), I used "-gtf22" option instead of "-gff3" and it worked fine in snpEff. ...
written 5 weeks ago by Vitis2.3k
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Answer: A: Visualizations of chimeric connections in different chromosomes
... I'd suggest querying the alignments and find inter-chromosomal chimeric connections and visualize them with circos. It is possible to visualize intra-chromosomal connections within the same framework. And the unusual ones, if those are what you're after, would stand out in circos plots. http://cir ...
written 5 weeks ago by Vitis2.3k
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Comment: C: Mutant Transcript is higher than the WT. What may be the reason?
... Comparing expression levels from IGV views is not very informative. You need to at least normalize against library size to compare expression levels of a genes across samples. ...
written 5 weeks ago by Vitis2.3k
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Comment: C: What is in your opinion the current state-of-the-art sequencing platform for gen
... I would support this comment with some real world experiences. I am working with one reference genome assembly assembled from PacBio and genetic map scaffolding. Homopolymer errors are very widely distributed and surprisingly common when the assembly is used in marker discovery and gene annotation, ...
written 6 weeks ago by Vitis2.3k
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Answer: A: Different alleles or paralogs?
... Technically, bacteria is "haploid", which means you can't have two "alleles" at the same locus. But biology always has exceptions. Sometimes, you have bacteria cells with multiple chromosomes, and at the same locus, the chromosomes can have different versions of the same gene. I think you'll have to ...
written 11 weeks ago by Vitis2.3k
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Comment: C: GATK JointDiscovery Error - Java Heap Space?
... Then I don't understand. Could you post this to GATK help forum? ...
written 12 weeks ago by Vitis2.3k
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Comment: C: GATK JointDiscovery Error - Java Heap Space?
... Did it give you the same "heap space" message and "RuntimeTotalMemory" after you specified 600G and ran the command? ...
written 12 weeks ago by Vitis2.3k

Latest awards to Vitis

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Voter 4 weeks ago, voted more than 100 times.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 8 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 8 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 10 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 11 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 13 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 14 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Great Question 2.9 years ago, created a question with more than 5,000 views. For Mapping Rates From Bwa
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 2.9 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: A Result From Mummer Alignment
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Housekeeping Gene Identifications
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Centurion 5.7 years ago, created 100 posts.
Guru 5.7 years ago, received more than 100 upvotes.
Supporter 5.7 years ago, voted at least 25 times.
Autobiographer 5.7 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 6.4 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler

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